Continental large igneous provinces are among the largest magmatic events on Earth, characteristically manifesting at the surface as stacks of monotonous flood basalt lavas that form through a dynamic pattern of eruptive pulses separated by hiatuses. Such dynamic patterns may be difficult to detect from the composition of the lavas. Instead, lava crystal cargoes can be used to study how the eruption cycles inherent to continental large igneous provinces are moderated by episodic recharge and evacuation at multiple crustal levels. Here, we present a stratigraphically well-constrained series of 56 flood basalt flows from the Eocene Initial Phase of magmatic activity in East Africa. These flows and their crystal cargo permit temporal insight into the development of one of the youngest and best-preserved continental large igneous provinces. The stratiform mafic lavas exposed in northern Kenya consist of alternating aphyric and plagioclase-phyric lava packages consistent with periods of eruption punctuated by volcanic hiatus, where magmas stall and crystallize plagioclase at medium to shallow crustal levels. Plagioclase compositions (n = 541) exhibit little intra-crystal or intra-sample compositional diversity. Intra-crystal equilibrium calculations for Sr and Ti indicate internal chemical equilibrium, requiring storage at high temperatures over a prolonged time interval (10 000–100 000 years). Using a series of seven interlinked partial crystal fractionation models under equilibrium conditions, we replicate the observed stratigraphic patterns in plagioclase composition. We find that the balance between recharge, evacuation, and diffusive equilibration within a shallow magmatic system controls the composition of plagioclase in these flood basalts. We conclude that the shallow fractionation system modulates eruptive cycles and thus constitutes a critical component in studies of continental large igneous provinces.